New Beginnings
by eternal iceheart
Summary: AU Story. When the expedition encounters a hidden legacy of the Ancients, events will unfold that show that the Tauri may be unprepared for the universe.
1. Chapter 1

**A Stargate Atlantis Fanfiction story – No infringement intended. All characters are the property of MGM.**

**Prologue**

How many centuries has it been since his exile? He has lost count of the years that have gone by since his fellow Wraith have banished him to live at the outer edge of the galaxy.

Fools. The queens and commanders of his hive were fools to fear the implications _– the benefits _- of his research. His way – his methods were so much more efficient, more effective than raiding human worlds every few centuries. They did not understand. All they cared were satisfying their hunger, to ensure other hives do not encroach on their territory and that no other species will become more dominant than them. No other ideals and goals were necessary. They had no interest in developing new avenues of research, no interest in exploring the empty edges of the galaxy or the hidden depths of the mind.

But that will change soon. He now had a fleet and an army, which evens the odds of going to battle with the Wraith hives.

He will wash away – burn away the decaying rotten structure that was Wraith society and build something better, stronger, _and cleaner_.

He wonders to himself - how has the galaxy changed in his absence?

**Chapter One**

Location: M340-1758

Training Camp

Sheppard's team made their way through the forest, following a well-trodden path, escorting two very important guests.

General O'Neil and Dr Daniel Jackson on an inspection tour as well as an evaluation mission to see if the Pentagon and the IOA's money were being well-spent. The training camp was the brainchild of some high-level think-tank at the Pentagon, taken from SG-1's reports on their encounter ten years ago with Apophis' infiltration camp with a bunch of kids playing at being SG-teams.

Gunfire, in the distance, causing O'Neil's hand to instinctively go for his side-arm.

"Probably the firing range", Sheppard commented. "MP-5s, by the sound of it", said Jackson. No surprise there. Even the most pacifistic civilian on any SG-team becomes a hardened soldier.

After twenty minutes, they came onto the camp, protected by two concentric circles, with a kilometer between each, the outer ring made of concertina razor wire and the inner ring, made up of sandbags.

Lots of tents, sandbags encampments, a few prefabricated buildings here and there, with soldiers in woodland pattern uniforms and black SWAT T-shirts completing make-shift obstacle courses, doing training exercises and running about, with the sound of combat boots crunching on the hard sand and gravel. Off in a distance, more soldiers in tactical vests and Kevlar helmets firing MP-5s, jumping in and out of trenches and ditches, firing blanks and intars too. The intars so kindly provided by the SGC.

One thing out of place, though. All the trainees were not from Earth. The instructors were Atlantis military personnel. A good number of trainees were Athosians, others were military representatives from Atlantis's most trusted trading partners and the rest were volunteers, human survivor from culled worlds, the sole survivors of their families, their only wish is to hurt the Wraith.

A proposed auxiliary militia, kind of a prototype, supporting the Tauri presence in the Pegasus, the consequence of Woolsey's negotiations during the trial of Sheppard's team by the Coalition, the camp an attempt to prove that the Tauri were not behaving like interfering overlords over the other human civilizations. The Coalition has tried to apply to send their representatives, and so has the Genii. Their application was still in process though, undergoing 'careful consideration' by Atlantis's leadership.

The proposed Pegasus militia, as it was already being called by some members of the expedition, was a controversial issue. The IOA and the Pentagon was in favor of the idea but not the SGC or the expedition, disliking putting MPS and M9s in the hands of people who didn't understood that the Atlantis expedition was always in danger of withdrawing back to Earth, because the costs outweigh the benefits of staying. There was also the consideration that creating a militia composed entirely of Pegasus natives did meant that the Atlantis expedition were behaving exactly like overlords, with the militia taking on the role of sepoy troops…

At the camp briefing room, after the customary tour was finished and afternoon tea with the recruits was done, an informal debate session was taking place. "This is dangerous", said Jackson, with Jack nodding in agreement. It was Ronon who speaks up in advance: "The people of this galaxy need to know that they can fight back, and the wraith need to know that their food can fight back", he growled. "How eloquent", said Rodney sarcastically, "Not exactly Shakespeare, but definitely theatre''. John just gave a snort, while Teyla said: "We are most grateful for your support, General, Doctor, but we feel that more can be done…"

"Such as?" pursed the general. "Well, a bigger budget could really help a lot, more trainers, expanding the camp into a proper training facility, more intars…", Sheppard said.

"How does this benefit Earth?", asked the General. "It gives hope", said Teyla. "Oh yeah, please elaborate on that _exactly helps Earth_", retorted the General. Before Teyla could further explain, they were interrupted by someone barging into the briefing room.

"Radio transmission from Atlantis by the Stargate", shouted an excited Lieutenant Kevin, new to Atlantis, gate travel and everything, unaware that life away from Earth is short and fraught...

**Chapter 2**

Back at Atlantis, Team Sheppard got ready to contact their allies in the Pegasus for information and the two distinguished guests got ready to board the Daedelus. The radio transmission was troubling. The Daedelus was being prepped with extra missiles and ammo for the railguns and a squad of Force Recon marines for Search and Rescue mission to Palandri for a missing medical team. The medical team sent to Palandri, was helping the ruling government there to handle their viral outbreak when the team sent a last transmission barely six hours ago showing an alien ship descending on the city going though the industrial revolution, and firing Wraith weaponry - the falling stars - on the city, burning buildings and the airships the Palandris use for transportation and travel to other cities. Wraith weaponry but not a wraith ship. A roughly spheroid shape, more like a potato actually, two and a half kilometer in diameter, hovering above the city and sending death below.

The Daedelus, making as planetary survey of the world Beneadral, due to the detection of nuclear tests on the surface, was attacked by another ship of the same design around the same time. The Asguard shields held. Sensor logs of the ship showed that the ship weren't Wraith in nature, except for the weapons. In fact, the hyperdrive signature and the hull material pointed towards Atlantean technology.

After six hours into the journey, Colonel Caldwell asked all senior staff to the mess room for a dinner. "Good steak", complimented General Jack, having dinner with Jackson and the senior officers of the Daedelus, everyone enjoying garlic-seasoned steak and a bottle of merlot provided, of all people, by Caldwell, known as the by-the-book Commanding Officer, since the presence of alcohol is forbidden on all frontline vessels, including those with space travel capability.

"Any ideas on who the new guys might be?" asked Daniel, after the table was cleared of dishes. "They're bad guys for sure, I mean, firing on defenseless cities and an unprovoked attack on the daedelus", Captain Jennings, the new commander of Daedelus' marine contingent said.

"Very hostile but we do not know their motives", put in Major Kevin, the Daedelus's new chief tactical officer.

"The mix of Wraith weaponry and atlantean propulsion indicates a technologically advanced civilization, to integrate mechanical hardware and biological hardware implies proficiency in understanding both technology, not that we can't achieve it", a somewhat arrogant statement by the chief science officer.

The debate went on, but everyone knew the lack of info was a hindering factor in making assumptions. Finally, the meeting broke and most went in for an early night of sleep.

Six hours later, the Daedelus dropped out of hyperspace. On the bridge, the crew looked at the viewscreen in shock.

"Sir, sensors shows three unidentified vessels holding position ten thousand meters on our starboard side! Seven more on our prow just three thousand meters ahead! Long-range sensors showing at least four more in this system!"

"Raise shields! All hands to battle stations! Open a hailing frequency!" Caldwell screamed. Suddenly, the Daedelus rocked violently. "Enemy fire! All shields holding!", Kevin shouted over the little fires that sprang up over the control boards of the bridge.

"They're not responding to our hails!"

"Return fire on all rail gun batteries! Helm, undertake evasive maneuvers! Set course on zero-seven, nine-zero mark at hundred and ten degrees angle and prepare a micro one-second jump to hyperspace on my command!"

"Enemy ships taking hits! They're showing substantial hull damage!"

"Jump now!"

The familiar blue of hyperspace appeared on the viewscreen on just a second and they were back in normal space, just thirteen thousand kilometers away.

"Get me a lock on their comm channels!" Caldwell ordered. Listening to the deep throated voices on the loudspeakers, everyone on the bridge realized what it was. "Wraith speech", Jackson said.

"They spotted us first! They moving to us at near light-speed!", disbelief clouding the tactical officer's voice. Few races could accelerate to near light-speed so fast, save for the ancients or the Asguard. "They're spreading into an enclosure pattern around us… and opening fire again!" The Daedelus started taking heavy fire again, but the enemy ships looked like they were having tiny pinpricks of fire all over them, the result of rail gun hits.

The General shouted "Colonel, we can't go up against fourteen ships!".

"Agreed! Sir!" Caldwell said "Jump to hyperspace now!"

The Daedelus jumped to safety, leaving the battlefield behind to fight another day.


	2. Chapter 2

Author's Note: This story is not only AU but it's going to be massively retconned as well from Stargate SG-1 Season 8 onwards.

This is one of my worst works; a rambling storyline without the focus or intensity I wanted. I blame my job for this.

**Back in Atlantis**

Mckay and the science team was briefing the General after a week of research while all Tauri forces in the Pegasus was placed on high alert.

"Using the scans we took of the enemy ship, we did a check on the Ancient database on the technology scans we took of the ship and it actually turned up in a file, that we're going through now; it's a huge file – ship specs, weapons design, pretty unconventional stuff. It doesn't seem to have the design aesthetics of the Ancients. Off-hand, its like some mad genius designed the specs."

"So the hostiles had some connection with the Atlanteans after all; and we're now clearing their messes again", commented Jackson.

Ignoring him, Mckay went on: "There is also a Stargate address in the file – a planet."

"Great news", General O'Neill said. "Prepare a team for reconnaissance mission. This mission could be hostile – use Marine Force Recon but send a UAV through first."

While Jack O'Neill had never interacted directly in the operations of Atlantis, he had a formidable reputation there, particularly with those that had worked in the SGC and those with Special Forces background. When a man like him gave an order, everybody literally jumped to their feet and got moving, partly out of respect and partly out of fear.

Within a hour, a UAV and a Marine reconnaissance team was prepped in the Atlantis gateroom and ready to go. Gathered within the Gateroom was the usual bunch of critical personnel. All watched as the Stargate address was dialed and a stable wormhole was established. The UAV was sent through amid much anticipation.

One of the technicians announced, "Telemetry from the UAY is coming through – breathable atmosphere, temperate climate, a forested terrain, and we're picking up artificial structures as well and – my god! Its incredibly huge – look at the size of that thing!"

On one of the screens was a visual transmission of the signals sent back of the UAV. In the distance was a building of hemisphere shape – a domed building. The UAV was equipped with ground aperture radar sensor pods – and the figures it sent back indicated that the dome was nearly a hundred meters high and had a diameter of three hundred meters.

Once the UAV gave indications of anything seemingly hostile; the Force Recon team was sent through and the wormhole was shut down. The Marines were expected to report back in thirteen hours. All Atlantis could do was wait.

They didn't wait long though. The eight marines that stepped back through the wormhole weren't tired – if anything, they looked fresh. And worried.

Their team leader, Captain Leonard, stepped forward to the General and told him, "Sir, what we've found can't wait"

The SGC team and Atlantis team gathered in the briefing room.

The video projector was running on the recording the Marines took on a camcorder on a projector screen.

It was the usual routine. The 2 km walk to the dome; the half-collapsed entrance; the spookiness that people back on Earth recognized as the 'Blair Witch Video Effect'.

It was the first skeleton they discovered at the entrance to the dome that was terrifying.

It wasn't wraith – and it wasn't human. Nearly two and a half meter tall, it was more Iratus bug than Wraith. What were disturbing were the elongated jaws that looked powerful enough to shred flesh and claws sharp enough to debowel a man.

The jaws and claws held the gleam of metal. They were artificial constructs.


	3. Chapter 3

**A Life in Ruins**

Back in the Atlantis cookhouse, the team that explored the dome was having their supper and gossiping at night while senior management was having their "Blair Witch Movie" session.

Sergeant Ben Lim, an American Chinese, of the Marine Corps, enjoyed such conversations. Having been in Atlantis nearly over a year, he was an anomaly in the Expedition: He thought he was in his own personal paradise.

Cafeteria talk soon revealed much of his personal history when he first arrived. He went to Paris Island for Basic when he was 19, did the marines for 5 years, left for a civilian life. He took up a degree in Australia, in the University of Queensland, in business, came back to the States and found a job in a bank.

Military life was hard but was easy to what Ben experienced in the corporate world. He was assigned by his company to customer service, or what is referred to by him personally as "the guys who take up the nonsense by idiot customers". Even worse, he was assigned to the customer service division, Asian branch.

That was really the low point of his life. He had to serve Asian businessmen, whom had the habit of behaving like feudal lords, to anybody who wasn't rich, the most blatant example of how money rules people lives. He lasted 2 years before quitting it and going back to the Corps. Military intelligence quickly spotted him as someone who might do well in Atlantis after a routine psychological profile test on selected military personnel.

There were 3 kinds of military personnel in Atlantis. The first kind was the people in the category known as high-performing achievers. They went to the right universities, came from the right families, went to West Point or Annapolis, did all the perfect assignments and knew the right Generals. They were capable but a good degree of their acceptance into Stargate operations were a matter of their privileged backgrounds. Most of them but not all were officers.

The second kind usually came from humble backgrounds, emotionally scarred childhoods or had life-breaking experiences but they were tough enough to claw their way to be known as the "success stories" of any organization. Almost universally NCOs, they were cynical, just smart and experienced enough to keep their mouths shut and look out for dangers to themselves and their men.

The third kind were the burnt-out cases. They ranged from corporals to Junior NCOs. They were formerly civilians who were pissed off by the stupidity of the human race in general. Most were social outcasts, loners and anti-socials. They were the ultimate cynics, disillusioned by life in both the civilian world and the military. They hated their superiors and everybody else in general, but obedience had been drilled enough into them to ensure that they always obey their orders, even though they approached life with a fatalistic attitude. Ben Lim was one of them.

Ben loved Atlantis. A fan of science fiction, he loved what he was doing, in no small part due to the fact that he was living practically in science fiction. Plus, he enjoyed freedom and autonomy he will never find elsewhere, not in the corporate world or in any military unit back on Earth side. The unique background setting mean that John Sheppard and other senior military commanders knew that they had to allow the men to blow off and had as much relaxation as possible or they'll be looking at frequent burnt-out cases.

Ben was eating lunch with his team when what was referred to in future reports as "Case Zero" happened. He was eating lunch halfway when suddenly, he started vomiting blood all over his spaghetti. His teammates quickly backed away from the table they were sitting at, staring at him in shock, attracting the attention of the entire cookhouse.

It was a macabre scene. First he vomited blood and dropped to his knees in front of the table. Then he started clawing his throat out. His skin turned a sickly yellow and a strange stench was present. It wasn't that of human waste but closer to that of rotting flesh.

Atlantis may have been old but it was still a technological building. In Tauri terminology, it was known as a 'smart city', complete with automation AI systems, running after millennia. The passages leading to the cookhouse was suddenly cut off by sliding bulkheads and all opened balconies and windows were similarly sealed shut.

Two hours later, a medical hazmat team managed to snuck into the cookhouse through the ventilation shafts by way of accessing from outside the auto-quarantined area through a carefully controlled airlock brought from the CDC 1 few years back when communication was re-established with Earth. It was made of plastic sheets and fiber-glass. By the time they got there, everyone in the cookhouse was dead.


End file.
